Human and HBV DGEs of SACC-PHHs mono-infected with HBV or coinfected with HBV/HDV_factors donor treatment_samples up to July 2018
Purpose:
To determine the DGE profiles (for human, HBV and HDV genes), relative to uninfected controls, of self-assembling co-cultures of primary human hepatocytes (SACC-PHHs) mono-infected with HBV or co-infected with HBV/HDV at 8 and 28 days post-infection. This run includes the samples sequenced in July 2018.
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
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## intersect, setdiff, setequal, unionlibrary(stringr)
library(ggplot2)
library(reshape2)
library(DESeq2)## Loading required package: S4Vectors## Loading required package: stats4## Loading required package: BiocGenerics## Loading required package: parallel##
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## lowesslibrary(dplyr)
library(RColorBrewer)
library(stringr)
library(genefilter)##
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library(ggrepel)
library(viridis)## Loading required package: viridisLitesource("http://bioconductor.org/biocLite.R")## Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help## A newer version of Bioconductor is available for this version of R,
## ?BiocUpgrade for helpbiocLite("org.Hs.eg.db")## BioC_mirror: https://bioconductor.org## Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.2 (2018-12-20).## Installing package(s) 'org.Hs.eg.db'## installing the source package 'org.Hs.eg.db'## Old packages: 'AMR', 'assertthat', 'backports', 'blob', 'boot', 'broom',
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## 'XML', 'xtable'require(org.Hs.eg.db)## Loading required package: org.Hs.eg.db## Loading required package: AnnotationDbi##
## Attaching package: 'AnnotationDbi'## The following object is masked from 'package:dplyr':
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## select## Function to perform DGE analysis with both donor and treatment set as factors influencing the counts.
DGE_analysis <- function(sampledirectory) {
a <- basename(Sys.glob(file.path(sampledirectory, "*.txt")))
sample_names <- sub('.txt', '', a)
##Here the donors are renamed based off the Hurel names (i.e. HU___) - RNASeq reads were all
##named using a different ID system.
sampleTable <- data.frame(sampleName = sample_names, sampleFile = a, treatment =
ifelse(grepl("Ctrl", a), "mock", ifelse(grepl("*co|*HDV", a),"coinf", "HBV")),
donor = ifelse(grepl("BD330*", a), "HU1019",
ifelse(grepl("BD405*", a), "HU1020",
ifelse(grepl("HU1016*", a), "HU1016", "HU1007"))),
time = ifelse(grepl("*D8|Day 8", a), "d8", "d28"),
replicate = ifelse(grepl("*sample_1h|*D8_ah|*D8_aa|*D8_am|*sample_1m", a), "a",
ifelse(grepl("*sample_2h|D28_bh|D28_ba|D28_bm|*sample_2m", a), "b",
ifelse(grepl("*sample_3h| * sample 1h|* sample 1m", a), "c",
ifelse(grepl("* sample 2h|* sample 2m", a), "d",
ifelse(grepl("* sample 3h|* sample 3m", a), "e", ""))))))
dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = sampledirectory,
design = ~donor + treatment)
dds
dds@colData
contrast <- c("treatment", levels(sampleTable$treatment))
output_basename <- sprintf("%s-%s_vs_%s_%s_analysis", "HumanHBVgenes", contrast[2],
contrast[3], levels(sampleTable$time))
output_basename
dds <- estimateSizeFactors(dds)
dds@colData
dds <- estimateDispersions(dds)
plotDispEsts(dds, main=sprintf("%s Dispersion Estimates", output_basename))
dds <- nbinomWaldTest(dds)
res <- results(dds, contrast=contrast)
res <- res[order(res$padj, -abs(res$log2FoldChange)),]
mcols(res, use.names=TRUE)
##Log-intensity ratios = M values, log-intensity averages = A values
##Red points indicate padj < 0.1.
plotMA(res, alpha=0.1, main=sprintf(output_basename))
attr(res, "filterThreshold")
metadata(res)$alpha
metadata(res)$filterThreshold
plot(metadata(res)$filterNumRej,
type="b", ylab="number of rejections",
xlab="quantiles of filter")
lines(metadata(res)$lo.fit, col="red")
abline(v=metadata(res)$filterTheta)
key = "ENSEMBL"
cols = c("ENTREZID", "SYMBOL", "GENENAME", "ALIAS", "REFSEQ", "ACCNUM")
for (col in cols) {
# Get annotation data for column
annotation_data <- AnnotationDbi::select(org.Hs.eg.db, rownames(res), col, keytype=key)
# Collapse one-to-many relationships
tmp <- aggregate(annotation_data[col], by=annotation_data[key],
# to a list
FUN=function(x)list(x))
# Match on key and append to results
idx <- match(rownames(res), tmp[[key]])
res[[col]] <- tmp[idx,col]
}
output_data <- as.data.frame(res)
LIST_COLS <- sapply(output_data, is.list)
for (COL in colnames(output_data)[LIST_COLS]) {
output_data[COL] <-
sapply(output_data[COL],
function(x)sapply(x, function(y) paste(unlist(y),
collapse=", ") ) )
}
# Save data frame above as tab-separated file
write.table(output_data,
file=file.path("Human DGEs_donortreatment", paste(Sys.Date(),
"human_donor_treatment",output_basename, "_results.txt", sep='')),
quote=FALSE, sep="\t", row.names=TRUE, col.names=NA)
return(list(dds@colData, head(res)))
}
##For each timepoint, determine the DGE profile when comparing the different treatments
##groups to one another (i.e. HBV-infected versus control).
##uninfected control cells versus those mono-infected with HBV
DGE_analysis("Human d8_ctrlvHBV")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 12 rows and 5 columns
## treatment donor time replicate
## <factor> <factor> <factor> <factor>
## BD330_Ctrl_D8humanHBVgenes mock HU1019 d8
## BD330_HBV_D8humanHBVgenes HBV HU1019 d8
## BD405A_Ctrl_D8humanHBVgenes mock HU1020 d8
## BD405A_HBV_D8humanHBVgenes HBV HU1020 d8
## Ctrl_D8_sample_1humanHBVgenes mock HU1007 d8 a
## ... ... ... ... ...
## HBV_D8_sample_1humanHBVgenes HBV HU1007 d8 a
## HBV_D8_sample_2humanHBVgenes HBV HU1007 d8 b
## HBV_D8_sample_3humanHBVgenes HBV HU1007 d8 c
## HU1016 Ctrl D8humanHBVgenes mock HU1016 d8
## HU1016_B_D8humanHBVgenes HBV HU1016 d8
## sizeFactor
## <numeric>
## BD330_Ctrl_D8humanHBVgenes 0.81649517899625
## BD330_HBV_D8humanHBVgenes 0.722206297298348
## BD405A_Ctrl_D8humanHBVgenes 0.535544074331218
## BD405A_HBV_D8humanHBVgenes 0.510842004431757
## Ctrl_D8_sample_1humanHBVgenes 1.8560572037995
## ... ...
## HBV_D8_sample_1humanHBVgenes 1.56574934988419
## HBV_D8_sample_2humanHBVgenes 1.10877923024603
## HBV_D8_sample_3humanHBVgenes 1.52270712654435
## HU1016 Ctrl D8humanHBVgenes 0.889277023545197
## HU1016_B_D8humanHBVgenes 0.523762795147403
##
## [[2]]
## log2 fold change (MLE): treatment HBV vs mock
## Wald test p-value: treatment HBV vs mock
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## AAB59969.1 2072.96301802315 10.4400443686251 0.452981751652525
## AAB59970.1 1565.31811760815 9.87162678928923 0.611933183516194
## AAB59972.1 190.005850792109 10.6311053508616 0.871839060142464
## AAB59971.1 161.867877694322 10.2941275823554 0.874365749561944
## ENSG00000187498 658.350424669 -1.50677233404892 0.191146706436798
## ENSG00000137801 1726.61042238045 -1.52493760532793 0.244484553722964
## stat pvalue
## <numeric> <numeric>
## AAB59969.1 23.0473839852019 1.56249540527572e-117
## AAB59970.1 16.1318703662489 1.52336244902277e-58
## AAB59972.1 12.1938851295839 3.35058197897517e-34
## AAB59971.1 11.7732511680755 5.36175411706471e-32
## ENSG00000187498 -7.88280563205583 3.20110807387631e-15
## ENSG00000137801 -6.23735766577673 4.45023705734201e-10
## padj ENTREZID SYMBOL
## <numeric> <list> <list>
## AAB59969.1 2.31389944567282e-113 NA NA
## AAB59970.1 1.12797372537891e-54 NA NA
## AAB59972.1 1.65395895088811e-30 NA NA
## AAB59971.1 1.98505541799028e-28 NA NA
## ENSG00000187498 9.48104189320685e-12 1282 COL4A1
## ENSG00000137801 1.09839267636963e-06 7057 THBS1
## GENENAME
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000187498 collagen type IV alpha 1 chain
## ENSG00000137801 thrombospondin 1
## ALIAS
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000187498 c("BSVD", "RATOR", "COL4A1")
## ENSG00000137801 c("THBS", "THBS-1", "TSP", "TSP-1", "TSP1", "THBS1")
## REFSEQ
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000187498 c("NM_001303110", "NM_001845", "NP_001290039", "NP_001836", "XM_011521048", "XP_011519350")
## ENSG00000137801 c("NM_003246", "NP_003237", "XM_011521971", "XP_011520273")
## ACCNUM
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000187498 c("AA678474", "AAA52006", "AAA52042", "AAA53098", "AAF72630", "AAH47305", "AAI42627", "AAI51221", "AAK53382", "AAK92480", "AAM97359", "AAP43112", "AB209646", "ABE73157", "ABX47006", "AF258349", "AF363672", "AF400431", "AF536207", "AH002650", "AY285780", "BAD92883", "BC047305", "BC142626", "BC151220", "BU677787", "CAA29075", "CAA31276", "CAA68698", "CD613007", "CN256264", "DQ464183", "EAX09108", "EAX09109", "EU260121", "H40591", "M11315", "NM_001303110", "NM_001845", "NP_001290039", "NP_001836", "P02462", \n"X03963", "X05561", "XM_011521048", "XP_011519350", "Y00706")
## ENSG00000137801 c("AAA21126", "AAA21127", "AAA36741", "AAA61178", "AAA61237", "AAB59366", "AAH28145", "AAI36470", "AAI36471", "AB209912", "AI147670", "AI168683", "AI290070", "AK291639", "AK293230", "AK304754", "AK309613", "AK310820", "AU117102", "AU279999", "BAD93149", "BAF84328", "BAG56769", "BAG65509", "BC015134", "BC028145", "BC136469", "BC136470", "BG115371", "BG251169", "BM512145", "BM784452", "BU676185", "CA411820", "CAA28370", "CAA32889", "CEF49520", "EAW92379", "EAW92380", "EAW92381", "LN607833", "M14326", \n"M25631", "M99425", "NM_003246", "NP_003237", "P07996", "X04665", "X14787", "XM_011521971", "XP_011520273")DGE_analysis("Human d28_ctrlvHBV")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 12 rows and 5 columns
## treatment donor time replicate
## <factor> <factor> <factor> <factor>
## BD330_Ctrl_D28humanHBVgenes mock HU1019 d28
## BD330_HBV_D28humanHBVgenes HBV HU1019 d28
## BD405A_Ctrl_D28humanHBVgenes mock HU1020 d28
## BD405A_HBV_D28humanHBVgenes HBV HU1020 d28
## Ctrl_D28_sample_1humanHBVgenes mock HU1007 d28 a
## ... ... ... ... ...
## HBV_D28_sample_1humanHBVgenes HBV HU1007 d28 a
## HBV_D28_sample_2humanHBVgenes HBV HU1007 d28 b
## HBV_D28_sample_3humanHBVgenes HBV HU1007 d28 c
## HU1016 Ctrl D28humanHBVgenes mock HU1016 d28
## HU1016_B_D28humanHBVgenes HBV HU1016 d28
## sizeFactor
## <numeric>
## BD330_Ctrl_D28humanHBVgenes 0.736034904845711
## BD330_HBV_D28humanHBVgenes 1.33827133500969
## BD405A_Ctrl_D28humanHBVgenes 0.438063892537815
## BD405A_HBV_D28humanHBVgenes 0.29006208835542
## Ctrl_D28_sample_1humanHBVgenes 2.33170342720659
## ... ...
## HBV_D28_sample_1humanHBVgenes 1.25484305155098
## HBV_D28_sample_2humanHBVgenes 1.67942007539527
## HBV_D28_sample_3humanHBVgenes 1.34803238058423
## HU1016 Ctrl D28humanHBVgenes 0.494723596467327
## HU1016_B_D28humanHBVgenes 0.461540433802861
##
## [[2]]
## log2 fold change (MLE): treatment HBV vs mock
## Wald test p-value: treatment HBV vs mock
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## AAB59969.1 1918.35454687059 8.88481993959276 0.339851221207296
## AAB59970.1 1556.99540930345 9.97502386577637 0.698181168571559
## AAB59972.1 172.626838978635 8.02490706391143 0.70802645868014
## AAB59971.1 115.521935885071 7.91293964574011 0.781597160225105
## ENSG00000183607 11.6836956046813 23.5901376915131 3.05874798852879
## ENSG00000134193 13.8351447468139 23.5071411915572 3.05867581138834
## stat pvalue
## <numeric> <numeric>
## AAB59969.1 26.1432632433396 1.17564477956107e-150
## AAB59970.1 14.2871568509714 2.63134746813491e-46
## AAB59972.1 11.3341909268066 8.88493579500364e-30
## AAB59971.1 10.1240639659708 4.32093131007735e-24
## ENSG00000183607 7.71235086381195 1.23520981758647e-14
## ENSG00000134193 7.68539807456329 1.52521994765974e-14
## padj ENTREZID SYMBOL
## <numeric> <list> <list>
## AAB59969.1 1.99906638316564e-146 NA NA
## AAB59970.1 2.2371716174083e-42 NA NA
## AAB59972.1 5.03598160860807e-26 NA NA
## AAB59971.1 1.83682789991388e-20 NA NA
## ENSG00000183607 4.20070154764808e-11 200504 GKN2
## ENSG00000134193 4.32247333166769e-11 83998 REG4
## GENENAME
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000183607 gastrokine 2
## ENSG00000134193 regenerating family member 4
## ALIAS
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000183607 c("BRICD1B", "GDDR", "PRO813", "TFIZ1", "VLTI465", "GKN2")
## ENSG00000134193 c("GISP", "REG-IV", "RELP", "REG4")
## REFSEQ
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000183607 c("NM_182536", "NP_872342")
## ENSG00000134193 c("NM_001159352", "NM_001159353", "NM_032044", "NP_001152824", "NP_001152825", "NP_114433")
## ACCNUM
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## AAB59972.1 NA
## AAB59971.1 NA
## ENSG00000183607 c("AAO85515", "AAQ89027", "AAY24521", "AF494509", "AJ966788", "AY358664", "AY943908", "BC110809", "CAI85014", "EAW99860", "NM_182536", "NP_872342", "Q86XP6")
## ENSG00000134193 c("AAG02562", "AAH17089", "AAK48435", "AAK59869", "AAM95598", "AAM95599", "AAM95600", "AF254415", "AF345934", "AK057107", "AY007243", "AY126670", "AY126671", "AY126672", "BC017089", "BF242936", "CAK22302", "EAW56711", "EAW56712", "EAW56713", "EAW56714", "NM_001159352", "NM_001159353", "NM_032044", "NP_001152824", "NP_001152825", "NP_114433", "Q9BYZ8")##uninfected control cells versus those co-infected with HBV and HDV
DGE_analysis("Human d8_ctrlvcoinf")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 16 rows and 5 columns
## treatment donor time
## <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes coinf HU1019 d8
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes coinf HU1019 d8
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes coinf HU1019 d8
## BD330_Ctrl_D8humanHBVgenes mock HU1019 d8
## BD330_HBV_HDV_D8_ahumanHBVgenes coinf HU1019 d8
## ... ... ... ...
## Ctrl_D8_sample_1humanHBVgenes mock HU1007 d8
## Ctrl_D8_sample_2humanHBVgenes mock HU1007 d8
## Ctrl_D8_sample_3humanHBVgenes mock HU1007 d8
## HU1016 Ctrl D8humanHBVgenes mock HU1016 d8
## HU1016_BD_co_D8humanHBVgenes coinf HU1016 d8
## replicate sizeFactor
## <factor> <numeric>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes c 0.859671712088571
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes d 0.882272381317184
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes e 1.26695172068585
## BD330_Ctrl_D8humanHBVgenes 0.819509720384803
## BD330_HBV_HDV_D8_ahumanHBVgenes a 1.22986508958441
## ... ... ...
## Ctrl_D8_sample_1humanHBVgenes a 1.83841145909955
## Ctrl_D8_sample_2humanHBVgenes b 1.78307849410724
## Ctrl_D8_sample_3humanHBVgenes c 2.00991925264611
## HU1016 Ctrl D8humanHBVgenes 0.9092752276918
## HU1016_BD_co_D8humanHBVgenes 0.66299189294213
##
## [[2]]
## log2 fold change (MLE): treatment coinf vs mock
## Wald test p-value: treatment coinf vs mock
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## AAB59969.1 3266.14780512167 9.68708598895568 0.567064755651631
## AAB59970.1 2161.46572239315 8.84798679338145 0.748279275076424
## ENSG00000091879 174.53783945627 -2.95489654935298 0.321724994358606
## ENSG00000179776 144.822437716892 -3.26901688675925 0.368693491000597
## AAB59972.1 510.491181909056 10.6166000723435 1.21355299663552
## AAB59971.1 480.567176685875 10.5410696087127 1.24030253361156
## stat pvalue
## <numeric> <numeric>
## AAB59969.1 17.0828567503264 1.99126284520909e-65
## AAB59970.1 11.8244445464266 2.91826614683191e-32
## ENSG00000091879 -9.18454145983867 4.13284322757718e-20
## ENSG00000179776 -8.86648928324572 7.54882038702633e-19
## AAB59972.1 8.7483613008885 2.16473222892492e-18
## AAB59971.1 8.49878906400265 1.9157866719377e-17
## padj ENTREZID SYMBOL GENENAME
## <numeric> <list> <list> <list>
## AAB59969.1 2.95543231485933e-61 NA NA NA
## AAB59970.1 2.16564530756396e-28 NA NA NA
## ENSG00000091879 2.04465530612335e-16 285 ANGPT2 angiopoietin 2
## ENSG00000179776 2.80098980460612e-15 1003 CDH5 cadherin 5
## AAB59972.1 6.42579114834073e-15 NA NA NA
## AAB59971.1 4.73901763081655e-14 NA NA NA
## ALIAS
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## ENSG00000091879 c("AGPT2", "ANG2", "ANGPT2")
## ENSG00000179776 c("7B4", "CD144", "CDH5")
## AAB59972.1 NA
## AAB59971.1 NA
## REFSEQ
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## ENSG00000091879 c("NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "XM_017013318", "XP_016868807")
## ENSG00000179776 c("NM_001114117", "NM_001795", "NP_001786", "XM_011522801", "XM_024450133", "XP_011521103", "XP_024305901")
## AAB59972.1 NA
## AAB59971.1 NA
## ACCNUM
## <list>
## AAB59969.1 NA
## AAB59970.1 NA
## ENSG00000091879 c("AAB63190", "AAF76526", "AAG17257", "AAI26201", "AAI26203", "AAI43903", "AAT69979", "AB009865", "AF004327", "AF187858", "AF218015", "AJ289780", "AJ289781", "AK075219", "AK225698", "AK290070", "AK310171", "AK312541", "BAA95590", "BAF82759", "BAG35440", "BC022490", "BC126200", "BC126202", "BC143902", "CAC08179", "CAC08180", "CAK96154", "DA829327", "EAW80472", "EAW80473", "EAW80474", "NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "O15123", "XM_017013318", \n"XP_016868807")
## ENSG00000179776 c("AAB41796", "AAH96363", "AAH96364", "AAH96365", "AAI17521", "AB035304", "AB209908", "AK300299", "AK300322", "AK300461", "BAA87418", "BAD93145", "BAG62052", "BAG62074", "BAG62180", "BC096363", "BC096364", "BC096365", "BC117520", "BQ716387", "CAA42468", "CAA56306", "DC381809", "DC382718", "EAW83009", "NM_001114117", "NM_001795", "NP_001786", "P33151", "U84722", "X59796", "X79981", "XM_011522801", "XM_024450133", "XP_011521103", "XP_024305901")
## AAB59972.1 NA
## AAB59971.1 NADGE_analysis("Human d28_ctrlvcoinf")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 16 rows and 5 columns
## treatment donor time
## <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes coinf HU1019 d28
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes coinf HU1019 d28
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes coinf HU1019 d28
## BD330_Ctrl_D28humanHBVgenes mock HU1019 d28
## BD330_HBV_HDV_D28_bhumanHBVgenes coinf HU1019 d28
## ... ... ... ...
## Ctrl_D28_sample_1humanHBVgenes mock HU1007 d28
## Ctrl_D28_sample_2humanHBVgenes mock HU1007 d28
## Ctrl_D28_sample_3humanHBVgenes mock HU1007 d28
## HU1016 Ctrl D28humanHBVgenes mock HU1016 d28
## HU1016_BD_co_D28humanHBVgenes coinf HU1016 d28
## replicate sizeFactor
## <factor> <numeric>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes c 0.755410636651868
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes d 0.664263202368975
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes e 0.688676521272185
## BD330_Ctrl_D28humanHBVgenes 1.20230358749222
## BD330_HBV_HDV_D28_bhumanHBVgenes b 0.932438545556839
## ... ... ...
## Ctrl_D28_sample_1humanHBVgenes a 3.71536586414676
## Ctrl_D28_sample_2humanHBVgenes b 3.84496101662567
## Ctrl_D28_sample_3humanHBVgenes c 4.26038252806512
## HU1016 Ctrl D28humanHBVgenes 0.822938518227753
## HU1016_BD_co_D28humanHBVgenes 0.897784791340134
##
## [[2]]
## log2 fold change (MLE): treatment coinf vs mock
## Wald test p-value: treatment coinf vs mock
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## AAB59969.1 1325.98744838806 7.8421423264979 0.577427162041115
## AAB59972.1 284.722709278814 7.31128552303804 0.68878635799948
## AAB59970.1 762.035637629851 7.47956672714904 0.739471482128307
## AAB59971.1 233.482411892535 8.15459391780692 0.937829843648784
## ENSG00000261371 314.622523632858 -2.11259427485376 0.400323405594147
## ENSG00000159189 8.59526020193391 -6.50545781928045 1.3948663152479
## stat pvalue
## <numeric> <numeric>
## AAB59969.1 13.5811801765216 5.1785239170969e-42
## AAB59972.1 10.6147362504 2.54512184374925e-26
## AAB59970.1 10.1147466912744 4.75244779226661e-24
## AAB59971.1 8.69517426112194 3.46297894578665e-18
## ENSG00000261371 -5.27721898178378 1.31159118616829e-07
## ENSG00000159189 -4.66385756696997 3.10336218958935e-06
## padj ENTREZID SYMBOL
## <numeric> <list> <list>
## AAB59969.1 1.17511064726763e-37 NA NA
## AAB59972.1 2.8876952439179e-22 NA NA
## AAB59970.1 3.59475151007046e-20 NA NA
## AAB59971.1 1.96454795594476e-14 NA NA
## ENSG00000261371 0.000595252543930618 5175 PECAM1
## ENSG00000159189 0.0117369158010269 714 C1QC
## GENENAME
## <list>
## AAB59969.1 NA
## AAB59972.1 NA
## AAB59970.1 NA
## AAB59971.1 NA
## ENSG00000261371 platelet and endothelial cell adhesion molecule 1
## ENSG00000159189 complement C1q C chain
## ALIAS
## <list>
## AAB59969.1 NA
## AAB59972.1 NA
## AAB59970.1 NA
## AAB59971.1 NA
## ENSG00000261371 c("CD31", "CD31/EndoCAM", "GPIIA'", "PECA1", "PECAM-1", "endoCAM", "PECAM1")
## ENSG00000159189 c("C1Q-C", "C1QG", "C1QC")
## REFSEQ
## <list>
## AAB59969.1 NA
## AAB59972.1 NA
## AAB59970.1 NA
## AAB59971.1 NA
## ENSG00000261371 c("NM_000442", "NP_000433", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", "XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000159189 c("NM_001114101", "NM_001347619", "NM_001347620", "NM_172369", "NP_001107573", "NP_001334548", "NP_001334549", "NP_758957")
## ACCNUM
## <list>
## AAB59969.1 NA
## AAB59972.1 NA
## AAB59970.1 NA
## AAB59971.1 NA
## ENSG00000261371 c("AAA36186", "AAA36429", "AAA60057", "AAB28645", "AAF91446", "AAF91447", "AAF91448", "AAF91449", "AAF91450", "AAF91451", "AAF91452", "AAF91453", "AAF91454", "AAF91455", "AAF91456", "AAF91457", "AAF91458", "AAF91459", "AAF91460", "AAH22512", "AAH51822", "AAK84009", "AAK84010", "AAK84011", "AF281287", "AF281288", "AF281289", "AF281290", "AF281291", "AF281292", "AF281293", "AF281294", "AF281295", "AF281296", "AF281297", "AF281298", "AF281299", "AF281300", "AF281301", "AF393676", "AF393677", "AF393678", \n"AFA36630", "AK091419", "AK290692", "AK303959", "AK304166", "BAF83381", "BAH14084", "BAH14122", "BC022512", "BC051822", "BC062608", "BG272085", "EAW94207", "EAW94208", "JQ287500", "M28526", "M37780", "NM_000442", "NP_000433", "P16284", "S66450", "X96849", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", \n"XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000159189 c("AAH09016", "AAP97191", "AF087892", "AK057792", "AK130613", "AK226152", "AL568589", "BAB71575", "BC009016", "BG060138", "BI824793", "CB995661", "CN480852", "DA849505", "EAW95016", "EAW95017", "EAW95018", "NM_001114101", "NM_001347619", "NM_001347620", "NM_172369", "NP_001107573", "NP_001334548", "NP_001334549", "NP_758957", "P02747")##monoinfected cells (HBV only) versus those co-infected with HBV and HDV
DGE_analysis("Human d8_coinfvHBV")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 16 rows and 5 columns
## treatment donor time
## <factor> <factor> <factor>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes coinf HU1019 d8
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes coinf HU1019 d8
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes coinf HU1019 d8
## BD330_HBV_D8humanHBVgenes HBV HU1019 d8
## BD330_HBV_HDV_D8_ahumanHBVgenes coinf HU1019 d8
## ... ... ... ...
## HBV_D8_sample_1humanHBVgenes HBV HU1007 d8
## HBV_D8_sample_2humanHBVgenes HBV HU1007 d8
## HBV_D8_sample_3humanHBVgenes HBV HU1007 d8
## HU1016_BD_co_D8humanHBVgenes coinf HU1016 d8
## HU1016_B_D8humanHBVgenes HBV HU1016 d8
## replicate sizeFactor
## <factor> <numeric>
## BD330 HBV_HDV Day 8 sample 1humanHBVgenes c 0.950093524498873
## BD330 HBV_HDV Day 8 sample 2humanHBVgenes d 0.976852312237081
## BD330 HBV_HDV Day 8 sample 3humanHBVgenes e 1.38937650643464
## BD330_HBV_D8humanHBVgenes 0.800900430466113
## BD330_HBV_HDV_D8_ahumanHBVgenes a 1.37494189687786
## ... ... ...
## HBV_D8_sample_1humanHBVgenes a 1.74127401206303
## HBV_D8_sample_2humanHBVgenes b 1.23394211692444
## HBV_D8_sample_3humanHBVgenes c 1.6932244461784
## HU1016_BD_co_D8humanHBVgenes 0.745371884953994
## HU1016_B_D8humanHBVgenes 0.572800938373677
##
## [[2]]
## log2 fold change (MLE): treatment coinf vs HBV
## Wald test p-value: treatment coinf vs HBV
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## ENSG00000091879 65.6382271456623 -2.3627591296235 0.370286768302615
## ENSG00000145692 562.152435832317 -3.06944724615823 0.518161314324531
## ENSG00000118785 74.3419325546154 -4.35619486978631 0.746983508976083
## ENSG00000142748 61.5785594794866 -3.952728196897 0.692060351818289
## ENSG00000243955 356.677353883194 -3.20710168421617 0.56322741641844
## ENSG00000116785 337.325779177824 5.50798937099992 1.04089769578811
## stat pvalue
## <numeric> <numeric>
## ENSG00000091879 -6.38088998009387 1.76061765484325e-10
## ENSG00000145692 -5.92372908070053 3.14721791218355e-09
## ENSG00000118785 -5.83171491397112 5.48605924956769e-09
## ENSG00000142748 -5.71153684286606 1.11960451548743e-08
## ENSG00000243955 -5.69415051669558 1.23987670394259e-08
## ENSG00000116785 5.29157610136661 1.21266709489556e-07
## padj ENTREZID SYMBOL
## <numeric> <list> <list>
## ENSG00000091879 1.53050492735524e-06 285 ANGPT2
## ENSG00000145692 1.36793826553058e-05 635 BHMT
## ENSG00000118785 1.58967710188306e-05 6696 SPP1
## ENSG00000142748 2.15564963747458e-05 8547 FCN3
## ENSG00000243955 2.15564963747458e-05 2938 GSTA1
## ENSG00000116785 0.00017015944964734 10878 CFHR3
## GENENAME
## <list>
## ENSG00000091879 angiopoietin 2
## ENSG00000145692 betaine--homocysteine S-methyltransferase
## ENSG00000118785 secreted phosphoprotein 1
## ENSG00000142748 ficolin 3
## ENSG00000243955 glutathione S-transferase alpha 1
## ENSG00000116785 complement factor H related 3
## ALIAS
## <list>
## ENSG00000091879 c("AGPT2", "ANG2", "ANGPT2")
## ENSG00000145692 c("BHMT1", "HEL-S-61p", "BHMT")
## ENSG00000118785 c("BNSP", "BSPI", "ETA-1", "OPN", "SPP1")
## ENSG00000142748 c("FCNH", "HAKA1", "FCN3")
## ENSG00000243955 c("GST-epsilon", "GST2", "GSTA1-1", "GTH1", "GSTA1")
## ENSG00000116785 c("CFHL3", "DOWN16", "FHR-3", "FHR3", "HLF4", "CFHR3")
## REFSEQ
## <list>
## ENSG00000091879 c("NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "XM_017013318", "XP_016868807")
## ENSG00000145692 c("NM_001713", "NP_001704")
## ENSG00000118785 c("NM_000582", "NM_001040058", "NM_001040060", "NM_001251829", "NM_001251830", "NP_000573", "NP_001035147", "NP_001035149", "NP_001238758", "NP_001238759")
## ENSG00000142748 c("NM_003665", "NM_173452", "NP_003656", "NP_775628")
## ENSG00000243955 c("NM_001319059", "NM_145740", "NP_001305988", "NP_665683", "XM_005249034", "XP_005249091")
## ENSG00000116785 c("NM_001166624", "NM_021023", "NP_001160096", "NP_066303", "XR_001736937", "XR_001736938", "XR_002958987", "XR_241062", "XR_426757")
## ACCNUM
## <list>
## ENSG00000091879 c("AAB63190", "AAF76526", "AAG17257", "AAI26201", "AAI26203", "AAI43903", "AAT69979", "AB009865", "AF004327", "AF187858", "AF218015", "AJ289780", "AJ289781", "AK075219", "AK225698", "AK290070", "AK310171", "AK312541", "BAA95590", "BAF82759", "BAG35440", "BC022490", "BC126200", "BC126202", "BC143902", "CAC08179", "CAC08180", "CAK96154", "DA829327", "EAW80472", "EAW80473", "EAW80474", "NM_001118887", "NM_001118888", "NM_001147", "NP_001112359", "NP_001112360", "NP_001138", "O15123", "XM_017013318", \n"XP_016868807")
## ENSG00000145692 c("AAC50668", "AAD22043", "AAH12616", "AAQ90058", "ACJ13646", "AK298308", "AK303780", "AK315224", "BAG37653", "BAG60562", "BAG64739", "BC012616", "BM678994", "DA370221", "EAW95831", "EAW95832", "EU794592", "NM_001713", "NP_001704", "Q93088", "U50929")
## ENSG00000118785 c("AA665210", "AAA17675", "AAA59974", "AAA86886", "AAC28619", "AAH07016", "AAH17387", "AAH22844", "AAH93033", "AAX59003", "AAY41035", "AB209987", "AB469789", "ABI63352", "ABI63357", "ABI63358", "AEA49027", "AEA49028", "AEA49030", "AEA49031", "AF052124", "AK057738", "AK075463", "AK290090", "AK290104", "AK295491", "AK296035", "AK315461", "ALE30613", "AY956318", "BAA03554", "BAA05949", "BAA05950", "BAA05951", "BAC11635", "BAE45628", "BAF82779", "BAF82793", "BAG37848", "BAG58801", "BAH12087", "BAH58215", \n"BC007016", "BC017387", "BC022844", "BC093033", "BF699765", "BX648003", "CAA31984", "CAX69239", "CB117856", "CBX54353", "D28759", "D28760", "D28761", "DA419665", "DQ839491", "DQ846870", "DQ846871", "EAX06004", "EAX06005", "EAX06006", "EAX06007", "EAX06008", "EAX06009", "EAX06010", "HQ874460", "HQ874461", "J04765", "JF412666", "JF412667", "KR062183", "M83248", "NM_000582", "NM_001040058", "NM_001040060", "NM_001251829", "NM_001251830", "NP_000573", "NP_001035147", "NP_001035149", "NP_001238758", "NP_001238759", \n"P10451", "X13694")
## ENSG00000142748 c("AAH20731", "AAQ88448", "AAQ88650", "AAU85296", "AK075140", "AK309540", "AK309576", "AY358081", "AY358283", "BAC11429", "BC020731", "BG546674", "CAF86408", "CAG33089", "CR456808", "EAX07756", "EAX07757", "NM_003665", "NM_173452", "NP_003656", "NP_775628", "O75636")
## ENSG00000243955 c("AAA35938", "AAA36174", "AAA52615", "AAA52618", "AAA70226", "AAB20973", "AAB24012", "AAH53578", "AAI10892", "AAT06769", "AEE60991", "AK293371", "AK310324", "AL096729", "AY532928", "BAH11495", "BC053578", "BC110891", "BG430521", "BI762344", "BM973137", "CA841071", "CAG28584", "CR407656", "DC339498", "EAX04385", "HM005393", "M14777", "M15872", "M21758", "M25627", "NM_001319059", "NM_145740", "NP_001305988", "NP_665683", "P08263", "S49975", "XM_005249034", "XP_005249091")
## ENSG00000116785 c("AAH20687", "AAH58009", "AAH70259", "AK298459", "BAG60672", "BC020680", "BC020687", "BC058009", "BC070259", "BG618529", "CAA48639", "CBN73475", "EAW91262", "EAW91263", "EAW91264", "NM_001166624", "NM_021023", "NP_001160096", "NP_066303", "Q02985", "X68679", "XR_001736937", "XR_001736938", "XR_002958987", "XR_241062", "XR_426757")DGE_analysis("Human d28_coinfvHBV")## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates
## 'select()' returned 1:many mapping between keys and columns## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## 'select()' returned 1:many mapping between keys and columns
## [[1]]
## DataFrame with 16 rows and 5 columns
## treatment donor time
## <factor> <factor> <factor>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes coinf HU1019 d28
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes coinf HU1019 d28
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes coinf HU1019 d28
## BD330_HBV_D28humanHBVgenes HBV HU1019 d28
## BD330_HBV_HDV_D28_bhumanHBVgenes coinf HU1019 d28
## ... ... ... ...
## HBV_D28_sample_1humanHBVgenes HBV HU1007 d28
## HBV_D28_sample_2humanHBVgenes HBV HU1007 d28
## HBV_D28_sample_3humanHBVgenes HBV HU1007 d28
## HU1016_BD_co_D28humanHBVgenes coinf HU1016 d28
## HU1016_B_D28humanHBVgenes HBV HU1016 d28
## replicate sizeFactor
## <factor> <numeric>
## BD330 HBV_HDV Day 28 sample 1humanHBVgenes c 0.830943677633343
## BD330 HBV_HDV Day 28 sample 2humanHBVgenes d 0.73384882041442
## BD330 HBV_HDV Day 28 sample 3humanHBVgenes e 0.758259958349027
## BD330_HBV_D28humanHBVgenes 2.40586075320506
## BD330_HBV_HDV_D28_bhumanHBVgenes b 1.03508949187203
## ... ... ...
## HBV_D28_sample_1humanHBVgenes a 2.24681866895274
## HBV_D28_sample_2humanHBVgenes b 2.97974367107981
## HBV_D28_sample_3humanHBVgenes c 2.34268177746246
## HU1016_BD_co_D28humanHBVgenes 0.999170705202106
## HU1016_B_D28humanHBVgenes 0.820750460492413
##
## [[2]]
## log2 fold change (MLE): treatment coinf vs HBV
## Wald test p-value: treatment coinf vs HBV
## DataFrame with 6 rows and 12 columns
## baseMean log2FoldChange lfcSE
## <numeric> <numeric> <numeric>
## ENSG00000164181 34.1842716459638 5.96558605992868 1.20287555737347
## ENSG00000113555 15.0279506409987 -4.65455014978377 1.02594551840299
## ENSG00000107719 18.7383368186678 -4.45503264715911 1.0136228349746
## ENSG00000261371 327.705448107525 -2.00936017105432 0.453858411643614
## ENSG00000176435 16.3727700489356 -4.6449069670697 1.07724213061943
## ENSG00000110799 209.794109113549 -2.82460115213463 0.70081645400404
## stat pvalue padj
## <numeric> <numeric> <numeric>
## ENSG00000164181 4.95943742755467 7.06976145135564e-07 0.0157415308475885
## ENSG00000113555 -4.53683949711982 5.71035318194246e-06 0.0616167816305245
## ENSG00000107719 -4.39515813322294 1.10692143412422e-05 0.0616167816305245
## ENSG00000261371 -4.42728419151156 9.54269688595705e-06 0.0616167816305245
## ENSG00000176435 -4.311850451299 1.61893922716199e-05 0.0720946016639779
## ENSG00000110799 -4.0304435433794 5.56716999376128e-05 0.206597678468481
## ENTREZID SYMBOL
## <list> <list>
## ENSG00000164181 79993 ELOVL7
## ENSG00000113555 51294 PCDH12
## ENSG00000107719 27143 PALD1
## ENSG00000261371 5175 PECAM1
## ENSG00000176435 161198 CLEC14A
## ENSG00000110799 7450 VWF
## GENENAME
## <list>
## ENSG00000164181 ELOVL fatty acid elongase 7
## ENSG00000113555 protocadherin 12
## ENSG00000107719 phosphatase domain containing, paladin 1
## ENSG00000261371 platelet and endothelial cell adhesion molecule 1
## ENSG00000176435 C-type lectin domain containing 14A
## ENSG00000110799 von Willebrand factor
## ALIAS
## <list>
## ENSG00000164181 ELOVL7
## ENSG00000113555 c("VE-cadherin-2", "VECAD2", "PCDH12")
## ENSG00000107719 c("KIAA1274", "PALD", "PALD1")
## ENSG00000261371 c("CD31", "CD31/EndoCAM", "GPIIA'", "PECA1", "PECAM-1", "endoCAM", "PECAM1")
## ENSG00000176435 c("C14orf27", "CEG1", "EGFR-5", "CLEC14A")
## ENSG00000110799 c("F8VWF", "VWD", "VWF")
## REFSEQ
## <list>
## ENSG00000164181 c("NM_001104558", "NM_001297617", "NM_001297618", "NM_024930", "NP_001098028", "NP_001284546", "NP_001284547", "NP_079206", "XM_005248606", "XM_005248607", "XM_006714695", "XM_011543651", "XM_017009885", "XM_017009886", "XM_017009887", "XM_017009888", "XM_017009889", "XP_005248663", "XP_005248664", "XP_006714758", "XP_011541953", "XP_016865374", "XP_016865375", "XP_016865376", "XP_016865377", "XP_016865378")
## ENSG00000113555 c("NM_016580", "NP_057664", "XM_024446106", "XP_024301874")
## ENSG00000107719 c("NM_014431", "NP_055246", "XM_011539637", "XM_011539638", "XM_017016072", "XP_011537939", "XP_011537940", "XP_016871561", "XR_001747093", "XR_945675")
## ENSG00000261371 c("NM_000442", "NP_000433", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", "XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000176435 c("NM_175060", "NP_778230")
## ENSG00000110799 c("NM_000552", "NP_000543")
## ACCNUM
## <list>
## ENSG00000164181 c("A1L3X0", "AAI30311", "AAI30313", "AB181393", "AI769834", "AK027216", "AL137506", "BAB15697", "BAD93238", "BC094792", "BC130310", "BC130312", "BC144257", "CAB70777", "DA247166", "EAW55001", "EAW55002", "NM_001104558", "NM_001297617", "NM_001297618", "NM_024930", "NP_001098028", "NP_001284546", "NP_001284547", "NP_079206", "XM_005248606", "XM_005248607", "XM_006714695", "XM_011543651", "XM_017009885", "XM_017009886", "XM_017009887", "XM_017009888", "XM_017009889", "XP_005248663", "XP_005248664", \n"XP_006714758", "XP_011541953", "XP_016865374", "XP_016865375", "XP_016865376", "XP_016865377", "XP_016865378")
## ENSG00000113555 c("AAF61931", "AAF73962", "AAH42634", "AAH52973", "AAQ88794", "AB026893", "AF231025", "AF240635", "AK023785", "AK024140", "AK027282", "AK226049", "AK315029", "AY358428", "BAA95162", "BAB14677", "BAB14837", "BAB55016", "BAG37515", "BC042634", "BC052973", "CA418447", "EAW61898", "NM_016580", "NP_057664", "Q9NPG4", "XM_024446106", "XP_024301874")
## ENSG00000107719 c("AAI36376", "AAI36377", "AB033100", "AK021806", "BAA86588", "BC015004", "BC040163", "BC048195", "BC136375", "BC136376", "CN335744", "EAW54404", "EAW54405", "EAW54406", "NM_014431", "NP_055246", "Q9ULE6", "XM_011539637", "XM_011539638", "XM_017016072", "XP_011537939", "XP_011537940", "XP_016871561", "XR_001747093", "XR_945675")
## ENSG00000261371 c("AAA36186", "AAA36429", "AAA60057", "AAB28645", "AAF91446", "AAF91447", "AAF91448", "AAF91449", "AAF91450", "AAF91451", "AAF91452", "AAF91453", "AAF91454", "AAF91455", "AAF91456", "AAF91457", "AAF91458", "AAF91459", "AAF91460", "AAH22512", "AAH51822", "AAK84009", "AAK84010", "AAK84011", "AF281287", "AF281288", "AF281289", "AF281290", "AF281291", "AF281292", "AF281293", "AF281294", "AF281295", "AF281296", "AF281297", "AF281298", "AF281299", "AF281300", "AF281301", "AF393676", "AF393677", "AF393678", \n"AFA36630", "AK091419", "AK290692", "AK303959", "AK304166", "BAF83381", "BAH14084", "BAH14122", "BC022512", "BC051822", "BC062608", "BG272085", "EAW94207", "EAW94208", "JQ287500", "M28526", "M37780", "NM_000442", "NP_000433", "P16284", "S66450", "X96849", "XM_005276880", "XM_005276881", "XM_005276882", "XM_005276883", "XM_011524889", "XM_011524890", "XM_017024738", "XM_017024739", "XM_017024740", "XM_017024741", "XP_005276937", "XP_005276938", "XP_005276939", "XP_005276940", "XP_011523191", "XP_011523192", \n"XP_016880227", "XP_016880228", "XP_016880229", "XP_016880230")
## ENSG00000176435 c("AAF28963", "AAH31567", "AAQ88761", "AAS77882", "AAT92280", "AF161403", "AY358395", "AY573061", "AY606132", "BC031567", "BX248017", "BX423057", "CAD62342", "EAW65835", "NM_175060", "NP_778230", "Q86T13")
## ENSG00000110799 c("AAA61293", "AAA61294", "AAA61295", "AAA65940", "AAB39987", "AAB59458", "AAB59512", "AAH22258", "AEY75227", "AF086470", "AK292122", "AK297600", "AK298097", "AK301216", "AW015780", "BAF84811", "BAG59985", "BAG60382", "BAG62791", "BC022258", "BG951111", "BQ898017", "CAA26503", "CAA27765", "CAA27972", "CAA29985", "CBX54458", "CCQ25771", "CD690980", "CDI44165", "DB293903", "EAW88814", "EAW88815", "EAW88816", "EAW88817", "EAW88818", "K03028", "M10321", "M17588", "NM_000552", "NP_000543", "P04275", "U81237", \n"X02672", "X04146", "X04385")Session Info
sessionInfo()## R version 3.5.2 (2018-12-20)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] parallel stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] org.Hs.eg.db_3.6.0 AnnotationDbi_1.44.0
## [3] BiocInstaller_1.30.0 viridis_0.5.1
## [5] viridisLite_0.3.0 ggrepel_0.8.0
## [7] data.table_1.12.0 genefilter_1.64.0
## [9] RColorBrewer_1.1-2 gplots_3.0.1
## [11] DESeq2_1.22.2 SummarizedExperiment_1.12.0
## [13] DelayedArray_0.8.0 BiocParallel_1.16.5
## [15] matrixStats_0.54.0 Biobase_2.42.0
## [17] GenomicRanges_1.34.0 GenomeInfoDb_1.18.1
## [19] IRanges_2.16.0 S4Vectors_0.20.1
## [21] BiocGenerics_0.28.0 reshape2_1.4.3
## [23] ggplot2_3.1.0 stringr_1.3.1
## [25] dplyr_0.7.8
##
## loaded via a namespace (and not attached):
## [1] bit64_0.9-7 splines_3.5.2 gtools_3.8.1
## [4] Formula_1.2-3 assertthat_0.2.0 latticeExtra_0.6-28
## [7] blob_1.1.1 GenomeInfoDbData_1.2.0 yaml_2.2.0
## [10] RSQLite_2.1.1 pillar_1.3.1 backports_1.1.3
## [13] lattice_0.20-38 glue_1.3.0 digest_0.6.18
## [16] XVector_0.22.0 checkmate_1.9.1 colorspace_1.4-0
## [19] htmltools_0.3.6 Matrix_1.2-15 plyr_1.8.4
## [22] XML_3.98-1.16 pkgconfig_2.0.2 zlibbioc_1.28.0
## [25] purrr_0.2.5 xtable_1.8-3 scales_1.0.0
## [28] gdata_2.18.0 tibble_2.0.1 htmlTable_1.13.1
## [31] annotate_1.60.0 withr_2.1.2 nnet_7.3-12
## [34] lazyeval_0.2.1 survival_2.43-3 magrittr_1.5
## [37] crayon_1.3.4 memoise_1.1.0 evaluate_0.12
## [40] foreign_0.8-71 tools_3.5.2 locfit_1.5-9.1
## [43] munsell_0.5.0 cluster_2.0.7-1 bindrcpp_0.2.2
## [46] compiler_3.5.2 caTools_1.17.1.1 rlang_0.3.1
## [49] grid_3.5.2 RCurl_1.95-4.11 rstudioapi_0.9.0
## [52] htmlwidgets_1.3 bitops_1.0-6 base64enc_0.1-3
## [55] rmarkdown_1.11 gtable_0.2.0 DBI_1.0.0
## [58] R6_2.3.0 gridExtra_2.3 knitr_1.21
## [61] bit_1.1-14 bindr_0.1.1 Hmisc_4.1-1
## [64] KernSmooth_2.23-15 stringi_1.2.4 Rcpp_1.0.0
## [67] geneplotter_1.60.0 rpart_4.1-13 acepack_1.4.1
## [70] tidyselect_0.2.5 xfun_0.4